**280**wrote:

Hello biostars,

I am trying to understand what rho means and how it is calculated in coalescent simulations. We know for Hundon's 'ms' program for example, that cross-over rate parameter is measured by 4N0 * r (r is probability of cross-over per generation between the ends of the locus). Now I want to simulate a locus in ms using -r parameter and I know average recombination rate for my species. How can I calculate per base per generation crossover rate?

Average recombination rate is in cM\Mb, so if, let's say, human recombination rate is 2 cM\Mb, genome size is 3 * 10^9 , then 2 / 1 * 10 ^6 = 2 * 10^-6 recombinations per base pair. This is way higher than a number used by default in different papers (such as 2*10^-8). And if I divide it by 3 * 10^9, the number is so small that it does not make sense at all. I know my calculations are incorrect, but I just don't see another way to derive this parameter.